Embodiments of the recent invention provide systems and methods for utilizing gene expression analysis for characterizing a biological condition or agent.
There has been substantial discussion including congressional hearings concerning medical errors. One source of medical errors include errors with medications. Upwards of 98,000 hospitalized patients annually have been documented to be victims of medication errors (Statement of the American Pharmaceutical Association to the Senate Appropriations Committee Labor, health and Human Services Education Subcommittee Hearing on Medical Errors Dec. 13, 1999). These errors include problems arising from drug interactions for a particular patient taking more than one drug, problems concerning the response of an individual to a particular drug and incorrect medication for a particular condition. Medical errors further arise as a result of misdiagnosis. This may occur as a result of insensitive diagnostic techniques or a wide range of interpersonal variability in the manner in which a clinical state is manifest. At present, there are few tools available for optimizing prognosis, diagnosis and treatment of a medical condition taking into account the particular phenotype and genotype of an individual.
There has been increasing interest in herbal drugs or nutraceuticals. These compounds are grown and collected from around the world, and consequently the compounds are subject to regional and temporal differences in collection and preparation that are difficult to control. It is frequently the case that one batch of a nutraceutical may be effective, there is no assurance that a second batch will be effective. Moreover. analysis of nutraceuticals is problematic because these drugs are complex mixtures in which little is known with respect to the active agent.
All new therapeutic agents require some form of clinical trials. It is known that a drug for treating tumor that is tested in a clinical trial using standard recruiting techniques for patients, may in fact show only limited efficacy. If the beneficial effect observed in a clinical population is too small, the drug will not receive approval by the Food and Drug Administration for use in the population at large. However, the small beneficial effect observed may in fact be an artifact of the clinical trial design or the clinical endpoint in the population of patients. It would be desirable to have criteria for screening patients as they enter a clinical trial to ensure that the beneficial effect of a drug if it exists may be detected and quantified.
In a first embodiment of the invention there is provided a method, for evaluating a biological condition of a subject, that includes: obtaining from the subject a sample having at least one of RNAs and proteins; deriving from the sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In another embodiment, a method is provided for evaluating a biological condition of a subject, that includes obtaining from the subject a first sample having at least one of fluid, cells and active agents; applying the first sample or a portion thereof to a defined population of indicator cells; obtaining from the indicator cells a second sample containing at least one of RNAs or proteins; deriving from the second sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In a another embodiment, a method is provided for evaluating a biological condition affected by an agent, the method including: obtaining, from a target population of cells to which the agent has been administered, a sample having at least one of RNAs and proteins; deriving from the sample a first profile data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition as affected by the agent.
In a another embodiment, a method is provided for evaluating the effect on a biological condition by a first agent in relation to the effect by a second agent, including: obtaining, from first and second target populations of cells to which the first and second agents have been respectively administered, first and second samples respectively, each sample having at least one of RNAs and proteins; deriving from the first sample a first profile data set and from the second sample a second profile data set, the profile data sets each including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing for the panel a first calibrated profile data set and a second profile data set, wherein (i) each member of the first calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a first baseline profile data set for the panel, and (ii) each member of the second calibrated profile data set is a function of a corresponding member of the second profile data set and a corresponding member of a second baseline profile data set for the panel, the calibrated profile data sets providing a measure of the effect by the first agent on the biological condition in relation to the effect by the second agent.
In a further embodiment, a method of conducting a clinical trial of an agent, is provided, including: causing the blind administration of a selected one of a placebo and the agent to each candidate of a pool of subjects; and using quantitative gene expression to monitor an effect of such administration.
In another embodiment, a digital storage medium is provided on which is stored a computer readable calibrated profile data set, wherein: the calibrated profile data set relates to a sample having at least one of RNAs and proteins derived from a target cell population to which an agent has been administered; the calibrated profile data set includes a first plurality of members, each member being a quantitative measure of a change in an amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of a biological condition as affected by administration of the agent.
In another embodiment, a digital storage medium is provided on which is stored a plurality of records Ri relating to a population of subjects, each record Ri corresponding to a distinct instance Pi of a computer readable profile data set P wherein: each instance Pi of the profile data set P relates to a distinct sample derived from a subject, the sample having at least one of RNAs and proteins; the profile data P set includes a plurality of members Mj, each member Mj being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of a biological condition; each record Ri includes, for each member Mij of a corresponding distinct instance Pi of the profile data set P, a value corresponding to the value of the member Mij; and each record Ri also includes a reference to a characteristic of the subject relative to the record, the characteristic being at least one of age group, gender, ethnicity, geographic location, diet, medical disorder, clinical indicator, medication, physical activity, body mass, and environmental exposure.
In a further embodiment, a digital storage medium is provided on which is stored a large number of computer readable profile data sets, wherein each profile data set relates to a sample derived from a target cell population to which has been administered an agent, the sample having at least one of RNAs and proteins; each profile data set includes a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of a biological condition; and the panel is the same for all profile data sets.
In a another embodiment of the invention, a method is provided for evaluating a biological condition of a subject, based on a sample from the subject, the sample having at least one of RNAs and proteins, the method including: deriving from the sample a first instance of a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and producing a first instance of a calibrated profile data set for the panel, wherein each member of an instance of the calibrated profile data set is a function of a corresponding member of an instance of the profile data set and a corresponding member of an instance of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject; accessing data in a condition database, the condition database having a plurality of records relating to a population of subjects, each record corresponding to a distinct instance of the calibrated profile data set; and evaluating the first instance of the calibrated profile data set in relation to data in the condition database.
In another embodiment of the invention, a method is provided of displaying quantitative gene expression analysis data associated with measurement of a biological condition, the method including: identifying a first profile data set pertinent to the gene expression analysis data, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject; and displaying the calibrated profile data set in a graphical format.
Another embodiment is directed to a descriptive record of a change in a biological condition, that includes: a first set of numerical gene expression values for a panel of gene loci, each value in the set corresponding to a single gene locus in a panel of gene loci, the set of values forming a profile data set for a population of cells subjected to a first biological condition; a second set of numerical gene expression values for the panel of gene loci, each value in the set corresponding to a single gene locus, the set of values forming a baseline profile data set for a second population of cells subjected to a second biological condition, the second set of values optionally being an average for multiple gene expression values from multiple populations of cells for each locus in the panel: and a third set of numbers corresponding to the ratio of the first set of values and the second set of values with respect to each gene locus in the panel, the third set being a calibrated profile data set; the profile data set and the calibrated profile data set being descriptive of the first biological condition with respect to the second biological condition.
In another embodiment, a method for diagnosing a biological condition of a subject is provided that includes: obtaining a sample from a subject; subjecting a population of cells to the sample and determining the presence of a first biological condition with respect to a second biological condition according to any of the above claims.
In another embodiment, a method is provided for diagnosing a susceptibility for a biological condition in a subject, that includes obtaining a sample from the subject; creating a descriptive record, according to the above, wherein the baseline set of values is an average of second values contained in a library of descriptive records for the second biological condition; the library containing a plurality of descriptive records grouped according to a predetermined biological condition; comparing the calibrated profile data set of the subject with the library of calibrated profile data sets and diagnosing the susceptibility of the subject.
In another embodiment, a method is provided for monitoring the progress of a biological condition, including: creating a plurality of descriptive records, according to the above; wherein each set of first values is determined at preselected time intervals with respect to the first record; comparing each calibrated profile data set with a library of calibrated profile data sets, the plurality of calibrated profile data sets being grouped according to a predetermined biological condition; and determining the progress of the biological condition with respect to gene expression.
In another embodiment, a method is provided for establishing the biological activity of a composition, including: selecting a population of cells; subjecting the cells to the composition; and determining the record according to the above description using a standardized baseline profile data set for the biological condition.
In another embodiment, a method is provided for determining which therapeutic agent from a choice of a plurality of therapeutic agents to administer to a subject so as to change a biological condition in a subject from a first biological condition to a second biological condition; including: subjecting a sample from the subject to each of a plurality of therapeutic agents; determining a descriptive record for each of the samples according to any of the above described methods, comparing each of the calibrated profile data sets to a library of calibrated profile data sets, the library of calibrated data sets being grouped according to a predetermined biological condition; and determining which of the therapeutic agents is capable of changing the first biological condition in the subject to the second biological condition in the subject.
In another embodiment, a method is provided for characterizing the biological effectiveness of a single batch of a composition produced by a manufacturing process, comprising: providing a fingerprint or signature profile according to any of the above methods; and labeling the batch of the composition by placing the fingerprint (signature profile) on each container in the batch.
In another embodiment, a method is provided for accessing biological information on a digital storage medium as described above, including: making the information available to a user.
In another embodiment, a method is provided for consumer evaluation of a product , wherein the consumer evaluation is dependent on a signature profile, including: identifying the product using the signature profile.
In another embodiment, a computer program product is provided for evaluating a biological condition of a subject or for evaluating a biological condition resulting from the use of an agent, including a computer usable medium having computer readable program code thereon, the computer program code; including: a program code for classifying a sample from the subject or the agent for an identifiable record; a program code for deriving a first data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; the profile data set being stored in the record; and a program code for optionally producing a calibrated profile data set for the panel, for storage in the record, each member of the calibrated profile data set being a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In another embodiment of the invention, a computer system for evaluating a biological condition of a subject or for evaluating a biological condition resulting from the use of an agent is provided, the computer system, including: a classification module for classifying a sample from the subject or the agent in an identifiable record; a derivative module for deriving a first data set, the first profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and a production module for producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In another embodiment, a method is provided for analyzing a patient for a biological condition at a remote site, including: providing a kit for measuring a profile data base for evaluating a biological condition, the kit including reagents for quantitative analysis of RNA or protein for a panel of gene loci; accessing a centralized database containing baseline profile data sets corresponding to the panel; determining the calibrated profile data set for the patient; and analyzing the biological condition of the patient.
Further embodiments of the invention include the use of calibrated profile data bases for determining the biological condition at one site in a subject from a sample taken from a second remote site. The biological condition may include disease, therapeutic interventions, aging, health conditioning and exercise, exposure to toxins, status of infection and health status. For example, calibrated precision profiles may be used to measure a biological condition(s) in one site (for example, the liver) by sampling cells from the same subject, but at a different site not generally considered a target for the biological condition, for example, peripheral blood cells in the case of liver disease.
Further embodiments of the invention include the use of calibrated profile data bases for determining the biological condition of the subject that includes placing a cell or fluid sample on indicator cells to assess the biological condition, the biological condition including disease, therapeutic interventions, aging, health conditioning and exercise, exposure to toxins, status of infection and health status.
Further embodiments of the invention include the use of calibrated profile data bases and profiles to assess, compare and contrast the bioactivities of therapeutic agents and therapeutic agent candidates including comparison of two agents having unknown properties; comparison of agents that are complex mixtures against those that are simple mixtures and comparisons of a single agent against a class of agents.
Further embodiments of the invention include the use of calibrated profile databases derived from in vitro dosing of an agent in indicator cells, or fluids or cells ex vivo to predict in vivo activities, activities including efficacy and toxicity and further permitting data on short term in vivo dosing of agent to predict long-term activities as described herein.
Another embodiment of the invention is at least one databases and its uses, the databases containing at least one of calibrated profile data sets and baseline profile data sets for discrete populations identified according to factors including diseases, geography, ethnicity, age and state of health.
A further embodiment of the invention is a database corresponding to an individual over time, the uses including managing a personalized health care program.
Additional embodiments include methods of running a clinical trial using calibrated profile data and databases containing calibrated profile data from in vitro and in vivo studies of the effect of the agent on populations of cells and methods of building a to clinical research network that uses calibrated profile data and traditional medical data.
Another embodiment of the invention provides a method, for evaluating a biological condition of a subject. This method includes:
a. obtaining from the subject a sample having at least one of RNAs and proteins;
b. deriving from the sample a first profile data set, the first profile dataset including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; and
c. producing a calibrated profile data set for the panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and a corresponding member of a baseline profile data set for the panel, the calibrated profile data set providing a measure of the biological condition of the subject.
In this embodiment, the biological condition relates to inflammation and the panel includes at least half, and, optionally, at least eighty percent of the constituents of the Inflammation Selected Panel of Table 1. In a related embodiment, the biological condition relates to cell growth and differentiation and the panel includes at least half, and optionally at least eighty percent, of the constituents of the Cell Growth and Differentiation Selected Panel of Table 2. In other related embodiments, the biological condition relates to metabolism and toxicity and the panel includes at least half, and optionally at least eighty percent, of the constituents of the Liver Metabolism and Toxicity Selected Panel of Tables 3 or 7. In another related embodiment, the biological condition relates to skin response and the panel includes at least half, and optionally at least eighty percent, of the constituents of the Skin Response Selected Panel of Table 4. In another related embodiment, the biological condition relates to the vascular system and the panel includes at least half, and optionally, at least eighty percent, of the constituents of the Vascular Selected Panel of Table 6. In a further related embodiment, the biological condition relates to the prostate health and disease and the panel includes at least half, and optionally at least eighty percent of the constituents of the Prostate Selected Panel of Table 5.
Another embodiment of the invention provides a method, for evaluating a biological condition of a subject, that includes: obtaining from the subject a sample having at least one of RNAs and proteins; deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; wherein such measurement is performed for each constituent under conditions wherein efficiencies of amplification for all constituents are substantially similar, the profile data set providing a measure of the biological condition of the subject.
Another embodiment of the invention provides a method, for evaluating a biological condition of a subject, that includes: obtaining from the subject a first sample having at least one of fluid, cells and active agents; applying the first sample or a portion thereof to a defined population of indicator cells; obtaining from the indicator cells a second sample containing at least one of RNAs or proteins; deriving from the second sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; wherein such measure is performed for each constituent under conditions wherein efficiencies of amplification for all constituents are substantially similar, the profile data set providing a measure of the biological condition of the subject.
Another embodiment of the invention provides method for evaluating a biological condition affected by an agent, the method that includes obtaining, from a target population of cells to which the agent has been administered, a sample having at least one of RNAs and proteins; deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables measurement of the biological condition; wherein such measure is performed for each constituent under conditions wherein efficiencies of amplification for all constituents are substantially similar, the profile data set providing a measure of the biological condition as affected by the agent.
Efficiencies of amplification of all constituents may differ by less than approximately 2%. The efficiencies of amplification may differ by less than approximately 1%. Moreover, in any of the embodiments of the invention described above which refers to a panel, the panel may include at least four constituents selected from any one of Tables 1 through 7. For example, at least four constituents may be selected from the group consisting of expression products of TNF-xcex1, IL-1-xcex1, IL-xcex2, IFN-xcex3, IL-8, and IL-10.
In another embodiment of the invention, a kit is provided having primer-probe combinations for measuring expression products of at least four constituents selected from any one of Tables 1 through 7. The kit may further include a primer probe combination constructed so as to hybridize only to at least one of cDNA and mRNA at a biologically relevant locus. Moreover, in each combination, a reverse primer may be selected which is complementary to a coding DNA strand located across an intron-exon junction, with not more than three bases of a three-prime end of the reverse primer being complementary to a proximal exon.